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Phylogenomics reveals the slow-burning fuse of diatom evolution

Alverson, Andrew J. LU ; Roberts, Wade R. ; Ruck, Elizabeth C. ; Nakov, Teofil ; Ashworth, Matthew P. ; Bryłka, Karolina LU orcid ; Downey, Kala M. ; Patrick Kociolek, J. ; Parks, Matthew and Pinseel, Eveline , et al. (2025) In Proceedings of the National Academy of Sciences of the United States of America 122(22).
Abstract

Evolution is often uneven in its pace and outcomes, with long periods of stasis interrupted by abrupt increases in morphological and ecological disparity. With thousands of gene histories, phylogenomics can uncover the genomic signatures of these broad macroevolutionary trends. Diatoms are a species-rich lineage of microeukaryotes that contribute greatly to the global cycling of carbon, oxygen, and silica, which they use to build elaborately structured cell walls. We combined fossil information with newly sequenced transcriptomes from 181 diverse diatom species to reconstruct the pattern, timing, and genomic context of major evolutionary transitions. Diatoms originated 270 Mya, and after >100 My of relative stasis in morphology and... (More)

Evolution is often uneven in its pace and outcomes, with long periods of stasis interrupted by abrupt increases in morphological and ecological disparity. With thousands of gene histories, phylogenomics can uncover the genomic signatures of these broad macroevolutionary trends. Diatoms are a species-rich lineage of microeukaryotes that contribute greatly to the global cycling of carbon, oxygen, and silica, which they use to build elaborately structured cell walls. We combined fossil information with newly sequenced transcriptomes from 181 diverse diatom species to reconstruct the pattern, timing, and genomic context of major evolutionary transitions. Diatoms originated 270 Mya, and after >100 My of relative stasis in morphology and ecology, a radiation near the Jurassic–Cretaceous boundary led to the diversity of habitats and cell wall architectures characteristic of modern diatoms. This transition was marked by a genome duplication and high levels of gene tree discordance. However, short generation times increase the probability of coalescence between speciation events, minimizing the impacts of incomplete lineage sorting and implicating sequence saturation and gene tree error as the main sources of discordance. Nevertheless, a rigorous tree-based approach to ortholog selection resulted in strongly supported relationships, including some that were uncertain previously. Three pulses of accelerated speciation were detected, two of which were associated with the evolution of novel traits and ecological transitions. The first 100 My of diatom evolution was a slow-burning fuse that led to a burst of innovations in ecology, morphology, and life history that are hallmarks of contemporary diatom assemblages.

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type
Contribution to journal
publication status
published
subject
keywords
concordance, discordance, diversification, incomplete lineage sorting, microbes
in
Proceedings of the National Academy of Sciences of the United States of America
volume
122
issue
22
article number
e2500153122
publisher
National Academy of Sciences
external identifiers
  • scopus:105007122160
  • pmid:40440071
ISSN
0027-8424
DOI
10.1073/pnas.2500153122
language
English
LU publication?
yes
id
88629880-466f-40ae-aa40-0208e0fe9932
date added to LUP
2025-07-28 10:38:04
date last changed
2025-07-29 03:00:03
@article{88629880-466f-40ae-aa40-0208e0fe9932,
  abstract     = {{<p>Evolution is often uneven in its pace and outcomes, with long periods of stasis interrupted by abrupt increases in morphological and ecological disparity. With thousands of gene histories, phylogenomics can uncover the genomic signatures of these broad macroevolutionary trends. Diatoms are a species-rich lineage of microeukaryotes that contribute greatly to the global cycling of carbon, oxygen, and silica, which they use to build elaborately structured cell walls. We combined fossil information with newly sequenced transcriptomes from 181 diverse diatom species to reconstruct the pattern, timing, and genomic context of major evolutionary transitions. Diatoms originated 270 Mya, and after &gt;100 My of relative stasis in morphology and ecology, a radiation near the Jurassic–Cretaceous boundary led to the diversity of habitats and cell wall architectures characteristic of modern diatoms. This transition was marked by a genome duplication and high levels of gene tree discordance. However, short generation times increase the probability of coalescence between speciation events, minimizing the impacts of incomplete lineage sorting and implicating sequence saturation and gene tree error as the main sources of discordance. Nevertheless, a rigorous tree-based approach to ortholog selection resulted in strongly supported relationships, including some that were uncertain previously. Three pulses of accelerated speciation were detected, two of which were associated with the evolution of novel traits and ecological transitions. The first 100 My of diatom evolution was a slow-burning fuse that led to a burst of innovations in ecology, morphology, and life history that are hallmarks of contemporary diatom assemblages.</p>}},
  author       = {{Alverson, Andrew J. and Roberts, Wade R. and Ruck, Elizabeth C. and Nakov, Teofil and Ashworth, Matthew P. and Bryłka, Karolina and Downey, Kala M. and Patrick Kociolek, J. and Parks, Matthew and Pinseel, Eveline and Theriot, Edward C. and Tye, Simon P. and Witkowski, Andrzej and Beaulieu, Jeremy M. and Wickett, Norman J.}},
  issn         = {{0027-8424}},
  keywords     = {{concordance; discordance; diversification; incomplete lineage sorting; microbes}},
  language     = {{eng}},
  number       = {{22}},
  publisher    = {{National Academy of Sciences}},
  series       = {{Proceedings of the National Academy of Sciences of the United States of America}},
  title        = {{Phylogenomics reveals the slow-burning fuse of diatom evolution}},
  url          = {{http://dx.doi.org/10.1073/pnas.2500153122}},
  doi          = {{10.1073/pnas.2500153122}},
  volume       = {{122}},
  year         = {{2025}},
}